Please take a look at our FAQ section and do not hesitate to report bugs or suggestions for improvements by email.

Address of the bookmark: https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

Applications are invited from individuals who have high motivation to do research for the below mentioned position,

1. Research Associate - 1 No.
in the DBT sponsored project under the supervision of Dr. D. Prabaharan, Principal Investigator, National Facility for Marine Cyanobacteria, Dept. of Marine Biotechnology, Bharathidasan University, Tiruchirappalli-24.

Title of the Project: “Establishment of National Repository for Micro algae & Cyanobacteria” funded by Department of Biotechnology, Govt. of India

Qualification

1. Research Associate – 1 No. Rs. 36,000/38,000/40,000 per month for I, II and III year + 20% HRA

Essential : Doctoral degree in relevant subject from recognized University/ Institutes
Desirable: Research experience in molecular biology and bioinformatics

Interested candidates can send their complete CV in plain paper with a passport size photograph, with details of Marks secured in all subjects from plus two stage (with proof, full postal address, sex, date of birth, community etc., along with additional qualification or experiences and two address of references whom could be contacted (One of whom should be PG teacher/guide). Application should reach the Principal Investigator on or before 30.06.2015 by Email (nfmcbic@yahoo.com)/Registered post/ Speed post, with subject subscribed as “Application for Research Associate /Technical Assistant /Lab attendant”. Qualifying candidates will be short listed and communicated with date of interview. No TA and DA will be given for attending the interview. Addressfor Communication Dr. D. Prabaharan Principal Investigator National Facility for Marine Cyanobacteria Bharathidasan University Tiruchirappalli-620024, Tamil Nadu.

Advertisement: http://www.bdu.ac.in/adv/NFMC_Project_Positions.pdf

https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Address of the bookmark: https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

We have sequenced the CHM13hTERT human cell line with a number of technologies. Human genomic DNA was extracted from the cultured cell line. As the DNA is native, modified bases will be preserved. The data includes 30x PacBio HiFi, 120x coverage of Oxford Nanopore, 70x PacBio CLR, 50x 10X Genomics, as well as BioNano DLS and Arima Genomics HiC. Most raw data is available from this site, with the exception of the PacBio data which was generated by the University of Washington/PacBio and is available from NCBI SRA.

A UCSC browser is available for v2.0 (as well as legacy v1.0 and v1.1 versions). An interactive dotplot visualization of all genomic repeats is also available from resgen.io. Known issues identified in the assembly are tracked at CHM13 issues.

MORE at https://github.com/marbl/CHM13

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

The candidate is expected to have experience in handling functional genomics tools to dissect defense responses against bacterial pathogens and drought stress tolerance. This project may involve use of bioinformatics tools, database development, large scale transcriptome profiling, virus-induced gene silencing and any other research work as assigned by the PI.

Qualification: Candidates having a Ph. D. degree in Bioinformatics/Plant Molecular Biology/Plant Physiology/Plant Pathology/Plant Breeding & Genetics and strong publication record can apply. Candidates having prior work experience in using advanced molecular biology tools in laboratory with strong bioinformatics knowledge are preferred.

The Fellowship amount for the position will be given at par with the similar fellowships by DBT/DST.

NIPGR reserves the right to select the candidate against the above post depending upon the qualifications and experience of the candidate. Reservation of post shall be as per Govt. of India norms.

Eligible candidates may apply by sending hard copy of complete application in the given format with a cover letter showing interest and specifying the position. The attested copies of the mark-sheets, certificates, proof of research experience/publications are to be attached. The application should reach at the address given below within 15 days from the date of advertisement. The envelope must be superscribed by "Application for the post of RA under NIPGR Short-term research fellowship programme". No TA/DA will be paid for attending the interview.

ONLY hard copy of the application in the given format will be accepted.
www.nipgr.res.in/files/careers/format_RA2.doc

Dr. Senthil-Kumar Muthappa
Staff Scientist - III,
National Institute of Plant Genome Research (NIPGR)
Aruna Asaf Ali Marg, P.O. Box NO. 10531,
New Delhi - 110067

Address of the bookmark: https://github.com/legumeinfo/gcv

More at http://biorg.cis.fiu.edu/

Features

• Circular and linear views of genomes

• Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

• Smooth zooming down to the sequence level

• Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

• Save high resolution PNG maps up to 8000x8000px

• Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

Assam Applications are invited for Walk-in-Interview for the following temporary positions in the MHRD sponsored Centre of Excellence under FAST project entitled “Machine Learning Research and Big Data Analysis” under the Principal Investigator Professor D.K. Bhattacharyya, Department of Computer Science & Engineering, Tezpur University.

Position : Senior Research Fellows (SRFs) in the field of (i) Bioinformatics (ii) Natural Language Processing / Speech Processing (iii) Cognitive Radio Networks / Optical Networks (iv) Network Security. No. of Positions : Five (05).

Qualification : First class in ME / M. Tech. in CSE / IT / ECE with research experience in relevant fields of research. Candidates having valid GATE / NET score shall be preferred.

Fellowship : Rs. 18,000/- (Rupees Eighteen Thousand) only per month.

Duration : Two (02) years and may be extended depending on status of the project.

Position : Junior Research Fellows (JRFs) in the field of Bioinformatics

No. of Positions : One (01).

Qualification : First class in B. Tech. in CSE / IT/ ECE or MCA with consistently good academic records. Candidates with M. Tech. in CSE / IT / ECE shall be preferred.

Fellowship : Rs. 12,000/- (Rupees twelve Thousand) only per month.

Duration : Two (02) years and may be extended depending on status of the project.

Interested candidates may send their application on plain paper by post along with his/her educational qualifications, research experience certificates (for Senior Research Fellow), 02 copies of recent passport/stamp size photograph and contact phone number to Prof. D.K. Bhattacharyya, Principal Investigator, Department of Computer Science & Engineering, Tezpur University, Napaam- 784028 or mail it to dkb@tezu.ernet.in (or to smh@tezu.ernet.in) within 15 days of publication of this advertisement.

Advertisement: www.tezu.ernet.in/ProjectWalkin/Advt_CoE_5816-A.pdf

What is Genome Assembly?

Genome assembly involves piecing together short DNA sequence reads generated by sequencing platforms (e.g., Illumina, PacBio, Oxford Nanopore) into longer, contiguous sequences called contigs. This can be performed as:

• De Novo Assembly: Without a reference genome.
• Reference-Guided Assembly: Using a reference genome to guide the assembly process.

Step 1: Preparing Your Data

Before starting the assembly, ensure that your raw sequencing data is high quality.

1. Input Data

   • Short Reads: Illumina sequencing generates short, accurate reads ideal for scaffolding.
   • Long Reads: PacBio and Nanopore sequencing provide long reads for resolving repetitive regions.

2. Quality Control (QC)
   Use tools like FastQC or MultiQC to assess the quality of your reads:

   fastqc reads.fastq multiqc .

   Look for issues like low-quality bases, adapter contamination, or overrepresented sequences.

3. Read Trimming and Filtering
   Trim low-quality bases and adapters using Trimmomatic or Cutadapt:

   trimmomatic PE reads_R1.fastq reads_R2.fastq trimmed_R1.fastq trimmed_R2.fastq \ ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36

Step 2: Choosing an Assembly Strategy

Select an assembly strategy based on your data type:

• Short-Read Assemblers:

  • SPAdes: Popular for microbial genomes.
  • Velvet: Fast for smaller genomes.

• Long-Read Assemblers:

  • Canu: Ideal for long-read datasets.
  • Flye: Versatile for small and large genomes.

• Hybrid Assemblers:

  • MaSuRCA: Combines short and long reads.
  • Unicycler: Optimized for bacterial genomes.

Step 3: Running the Assembly

3.1. SPAdes (Short-Read Assembly)

SPAdes is an excellent choice for small genomes, such as bacteria.

The output includes assembled contigs (contigs.fasta) and scaffolds (scaffolds.fasta).

3.2. Canu (Long-Read Assembly)

Canu is designed for high-error long reads from PacBio or Nanopore.

The output will be in canu_output/genome.contigs.fasta.

3.3. Hybrid Assembly with Unicycler

Unicycler combines short and long reads for improved assemblies.

Step 4: Assessing Assembly Quality

After assembly, evaluate its quality using the following tools:

1. QUAST
   QUAST generates assembly statistics, such as N50, genome size, and GC content:

   quast contigs.fasta -o quast_output

2. BUSCO
   BUSCO checks genome completeness by identifying conserved genes:

   busco -i contigs.fasta -o busco_output -l fungi_odb10 -m genome

3. Assembly Graph Visualization
   Visualize assembly graphs with Bandage:

   Bandage load assembly_graph.gfa

Step 5: Post-Assembly Steps

1. Polishing
   Improve assembly accuracy using tools like Pilon (for short reads) or Racon (for long reads).

   racon long_reads.fasta mapped_reads.sam contigs.fasta > polished_contigs.fasta

2. Scaffolding
   Link contigs into scaffolds using tools like SSPACE or Opera-LG if required.

3. Annotation
   Annotate the assembled genome using Prokka for prokaryotes or Maker for eukaryotes.

   prokka --outdir annotation_output --prefix genome contigs.fasta

Step 6: Sharing and Archiving

1. Submit to Public Repositories
   Share your assembly in databases like NCBI GenBank, ENA, or DDBJ.

2. Metadata Preparation
   Include detailed metadata for your submission, such as organism name, sequencing platform, and coverage.

Best Practices

• Always perform quality checks at each stage to ensure data integrity.
• Use multiple tools to cross-validate results when working with complex genomes.
• Document parameters and software versions for reproducibility.

Conclusion

Genome assembly is a powerful process that transforms raw sequencing data into a coherent representation of an organism’s genome. By following this step-by-step guide, you can successfully assemble genomes and uncover valuable biological insights. Whether you’re assembling a microbial genome or tackling the complexities of a eukaryotic genome, these tools and strategies will set you on the path to success.